I want to use a relative file path as a command line argument but as the example and assessment below will demonstrate, the variable passes \..\ as a string, it doesn't evaluate it.
Can I can force the command line to parse and expand the variable as a string?
: For example: I have a R script file I want to launch from the command line:
Set RPath=C:\Program Files\R\R-3.1.0\bin\Rscript.exe
SET RScript=%CD%\..\..\HCF_v9.R
SET SourceFile=%CD%\..\Source\
ECHO String used for Source Location - %SourceFile%
"%RPath%" "%RScript%" %SourceFile%
The inclusion of \..\ works in the call to R as an external program because the batch file can resolve it's own commands.
The variable of SourceFile however doesn't work because the SourceFile variable hasn't expanded \..\, it has just included it as part of the string and R can't process \..\
You can use the for replaceable parameters to resolve to the real path
for %%a in ("..\..\HCF_v9.R") do set "RScript=%%~fa"
#MC ND has provided the batch file approach; an R-centric approach would be to pass the current directory to R, and modify it there.
; batch file
Set RPath=C:\Program Files\R\R-3.1.0\bin\Rscript.exe
SET RScript=%CD%\..\..\HCF_v9.R
"%RPath%" "%RScript%" %CD%
# in R
srcpath <- commandArgs(TRUE)[1]
srcpath <- normalizePath(file.path(srcpath, "../Source"))
Related
I'd like to create a log file which is named after the originally run Julia file, for example here julia foo.jl I'd want foo.jl. From within a Julia session how can I get this information>
The global constant PROGRAM_FILE is set to the script name.
This can be done by inspecting the stack
# first get the top of the stack
f = stacktrace()[1]
# then get the file's name as a string, note the is absolute.
abs_filename = String(f.file)
println(abs_filename)
# to get only the filename use
println(basename(abs_filename))
I have a test.jl Julia script file in a directory, e.g., /home/directory1. Assume that I want to save the output of this code as a .txt file in the same directory. My problem is that, obviously, the .txt file will be saved in the working directory of Julia, which by pwd() is somewhere else, e.g., /home/julia/.
I wonder how can I change the working directory in the test.jl script WITHOUT writting the directory address, /home/directory1 , manually? I know that I can change the working directory by cd("/home/directory1"), but the problem is that I don't want to write the address manually. Is there any way to get the directory address of test.jl within itself by a command?
You can get that information using macro #__FILE__
help?> #__FILE__
#__FILE__ -> AbstractString
Expand to a string with the path to the file containing the macrocall, or an empty string if evaluated by julia -e <expr>. Return nothing if the macro was missing parser source information. Alternatively see PROGRAM_FILE.
Example:
julia> open("c:\\temp\\some.jl","w") do f
println(f, "println(\"Running at \$(#__FILE__)\")")
end
julia> include("c:\\temp\\some.jl")
Running at c:\temp\some.jl
shell> julia "c:\temp\some.jl"
Running at c:\temp\some.jl
Working with Fortran90 in Unix...
I have a programme which needs to read in the input parameters from a file "input-deck.par". This filename is currently hard-coded but I want to run a number of runs using different input-deck files (input-deck01.par, input-deck02.par, input-deck03.par etc.) so I've set-up the code to do a simple "read(*,*) inpfile" to allow the user to input the name of this file directly on run-time with a view to scripting this later.
This works fine interactively. If I execute the programme it asks for the file name, you type it in and the filename is accepted, the file is opened and the programme picks up the parameters from that file.
The issue lies in scripting this. I've tried scripting using the "<" pipe command so:
myprog.e < input-deck01.par
But I get an error saying:
Fortran runtime error: Cannot open file '----------------': No such file or directory
If I print the filename right after the input line, it prints that the filename is '----------------' (I initialise the variable as having 16 characters hence the 16 hyphens I think)
It seems like the "<" pipe is not passing the keyboard input in correctly. I've tried with spaces and quotes around the filename (various combinations) but the errors are the same.
Can anyone help?
(Please be gentle- this is my first post on SO and Fortran is not my primary language....)
Fortran has the ability to read the command line arguments. A simple example is
program foo
implicit none
character(len=80) name
logical available
integer fd
if (command_argument_count() == 1) then
call get_command_argument(1, name)
else
call usage
end if
inquire(file=name, exist=available)
if (.not. available) then
call usage
end if
open(newunit=fd, file=name, status='old')
! Read file
contains
subroutine usage
write(*,'(A)') 'Usage: foo filename'
write(*,'(A)') ' filename --> file containing input info'
stop
end subroutine usage
end program foo
Instead of piping the file into the executable you simply do
% foo input.txt
I need to achieve the below using Robotframework script:
c:\>runbatch "C:\Program Files (x86)\tool\bin\test.exe" C:\tool\get.ini
where runbatch is a MS DOS Batch and "C:\Program Files (x86)\tool\bin\test.exe" and C:\tool\get.ini are parameters to the batch file. The first argument contains path of a tool that has "(" and ")" in its path.
So in my Robot script I have a variable like below:
${tool_path} "C:\\Program Files (x86)\\tool\\bin\\test.exe"
${tool_ini} "C:\tool"
And invoke like below:
${RC}= Run Process ${CURDIR}/../scripts/runbatch.bat ${tool_path} ${tool_ini}\\get.ini
The execution fails but note when I run it via the same param thru the command line as standalone batch it works fine.
In the batch I added comments to just log the arguments and I found that they are completely distorted, the tool_path value is completely distorted ("\"C:\Program) and second argument becomes (Files ) - how can I fix the issue in robot script such that when a path is passed having braces are not modified?
You need to also escape the backslashes in ${tool_ini} - make its value c:\\tool; that's not the culprit thought, just something else to change.
Remove the double quotes in the arguments' values - Run Process does not need them in the way you are calling it, with a keyword argument per script argument. E.g.:
${tool_path} C:\\Program Files (x86)\\tool\\bin\\test.exe
${tool_ini} C:\\tool
${RC}= Run Process ${CURDIR}/../scripts/runbatch.bat ${tool_path} ${tool_ini}\\get.ini
The way you've put them, they have become a part of the value itself.
Alternatively, keeping the double quotes there, you can call the script with all arguments in the call line:
${tool_path} "C:\\Program Files (x86)\\tool\\bin\\test.exe"
${tool_ini} C:\\tool
${RC}= Run Process ${CURDIR}/../scripts/runbatch.bat ${tool_path} "${tool_ini}\\get.ini"
(the second one doesn't really need quotes, but I've added them for consistency)
By the way, not really an issue, yet - the script path uses slashes (/), which is a bit unorthodox for Windows. Contrary to the popular believe, the OS does support this path delimiter pretty much the same way as it supports backslashes (\), it's just not widely used and looks a bit out of place.
I am writing a CGI script in Perl with a section of embedded R script which produces a graph. The original data filename is unknown as it has been uploaded by the CGI script and is stored in a Perl variable called $filename.
My question is that I now would like to open that file in R using read.table(). I am using Statistics::R and so I have tried:
my $R = Statistics::R->new();
$R->set('filename',$filename);
my $out1 = $R->run(
q`rm(list=ls())`,
# Fetch data
q`setwd("/var/www/uploads")`,
q`peakdata<-read.table(filename, sep="",col.names=c("mz","intensity","ionsscore","matched","query","index","hit"))`,
q`attach(peakdata)` ...etc
I can get this to work ONLY if I change $filename into something static and known like 'data.txt' before trying to open the file in read.table - is there a way for me to open a file with a variable for a name?
Thank you in advance.
One possible way to do this is by doing a little more work in Perl.
This is untested code, to give you some ideas:
my $filename = 'fileNameIGotFromSomewhere.txt'
my $source_dir = '/var/www/uploads';
my $file = "$source_dir/$fielname";
# make sure we can read it
unless ( -r $file ) {
die 'can read that data file: $!";
}
Then instead of $R->set, you could interpolate the file name into the R program. Where you've used the single-quote operator, use the double-quote operator instead:
So instead of:
q`peakdata<-read.table(filename, sep="",col.names= .... )`
Use:
qq`peakdata<-read.table($filename, sep="",col.names= .... )`
Now this looks like it would be inviting problems similar to SQL/Code Injections, so that's why I put int the logic to insure that the file exists and is readable. You might be able to think other checks to add to safeguard your use of user-supplied info.